The use of oligonucleotide arrays in nucleic acid detection and sequencing, and in particular for clinical diagnosis, is a rapidly growing field. Generally, an oligonucleotide array is comprised of a number of individual oligonucleotides linked to a solid support in a regular pattern, each one in a different area, so that the location of each oligonucleotide is known. After generation of the array, samples containing the target sequences are exposed to the array, hybridized to the complementing oligonucleotides bound in the array, and the hybridized sequences are detected using a wide variety of methods, most commonly radioactive or fluorescent labels.
Currently there are a variety of technologies available to generate oligonucleotide arrays. Generally, the arrays are prepared by synthesizing all of the oligonucleotides simultaneously on the solid support, using solid-phase synthesis combined with some type of masking or chemical protection to allow for the selective addition of the nucleotides at any particular position. A preferred method uses photolithographic techniques. Alternatively, micro-dispensing of oligonucleotides onto functionalized solid supports is done.
However, there are a number of problems associated with this type of synthesis. In particular, when every addition of every nucleotide is a separate reaction on a single solid support, the reproducibility and yield may vary widely as between different locations on the support, as well as between supports. Micro-dispensing can also show variability. Additionally, the equipment and materials need to generate the arrays can be quite costly.
Accordingly, it is an object of the invention to provide oligonucleotide arrays which can be easily generated and are highly reproducible, and methods of using such arrays.